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### Running command:
###
###   chmod a+r HiCDCPlus -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data HiCDCPlus
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* checking for file 'HiCDCPlus/DESCRIPTION' ... OK
* preparing 'HiCDCPlus':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'HiCDCPlus.Rmd' using rmarkdown
Loading required package: BSgenome
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
Using chr21and cut patterns GATC
Joining, by = "bins"
Joining, by = "bins"
Joining, by = "bins"
Using chr22and cut patterns GATC
Joining, by = "bins"
Joining, by = "bins"
Joining, by = "bins"
WARN [2022-04-12T11:21:23,440]  [Globals.java:138] [main]  Development mode is enabled
Chromosome chr21 intrachromosomal counts processed.
WARN [2022-04-12T11:21:33,558]  [Globals.java:138] [main]  Development mode is enabled
Chromosome chr22 intrachromosomal counts processed.
Chromosome chr21 complete.
Chromosome chr22 complete.
WARN [2022-04-12T11:21:39,929]  [Globals.java:138] [main]  Development mode is enabled
Using 1 CPU thread(s)
Not including fragment map
Start preprocess
Writing header
Writing body
...
Writing footer

Finished preprocess

Calculating contact matrices took: 3875 milliseconds
No normalization vectors

Calculating norms for zoom BP_50000c1 1 c2 1
c1 2 c2 2
c1 3 c2 3
c1 4 c2 4
c1 5 c2 5
c1 6 c2 6
c1 7 c2 7
c1 8 c2 8
c1 9 c2 9
c1 10 c2 10
c1 11 c2 11
c1 12 c2 12
c1 13 c2 13
c1 14 c2 14
c1 15 c2 15
c1 16 c2 16
c1 17 c2 17
c1 18 c2 18
c1 19 c2 19
c1 20 c2 20
c1 21 c2 21
VC and VC_SQRT normalization of 21 at BP_50000 took 62 milliseconds
KR normalization of 21 at BP_50000 took 266 milliseconds
29
1.0E-4
0.0
[14.67025359153608, 8.391197915657669, 3.372272978434605, 1.3243679789048493, 0.5014996451770486, 0.18015729321366436, 0.0582865791102698, 0.014088943425846878, 0.003198391114459298, 0.004522741429202171, 0.004822016796751427, 0.004112180789068276, 0.003282358605993352, 0.0025864277714511275, 0.002060714672836639, 0.0016782392031444715, 0.0014018819119208104, 0.0012000998731203083, 0.0010496580626124796, 9.344696239317329E-4, 8.437144579005462E-4, 7.701976966032476E-4, 7.091363498616943E-4, 6.573251785937373E-4, 6.125841840045609E-4, 5.733998811514596E-4, 5.386947840548828E-4, 5.0767989437972E-4, 4.797602742243612E-4, 0.0, 4.797602742243612E-4, 0.0014944086204946583, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
SCALE normalization of 21 at BP_50000 took 78 milliseconds
c1 22 c2 22
VC and VC_SQRT normalization of 22 at BP_50000 took 16 milliseconds
KR normalization of 22 at BP_50000 took 94 milliseconds
30
1.0E-4
0.0
[1.1616125492660587, 0.3248634711785725, 0.03887833349214653, 0.013686919557396537, 0.005116232178192792, 0.002028650228928619, 0.0010228250709780617, 8.204523605293002E-4, 6.822216825863592E-4, 5.816929345858757E-4, 5.048685132782449E-4, 4.437633451610523E-4, 3.9363251275847944E-4, 3.515395884994277E-4, 3.155862639041551E-4, 2.844890392816879E-4, 2.573412738098302E-4, 2.3347590528177697E-4, 2.1238399417500275E-4, 1.9366496189565652E-4, 1.769952728143398E-4, 1.6210811820993598E-4, 1.4877982509520216E-4, 1.3682047578789103E-4, 1.2606722823016447E-4, 1.1637941138320507E-4, 1.0763481703612854E-4, 9.972681922221227E-5, 9.256208169983182E-5, 8.605869477995576E-5, 0.0, 8.605869477995576E-5, 0.001757524231016605, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
SCALE normalization of 22 at BP_50000 took 47 milliseconds
c1 X c2 X
c1 Y c2 Y
c1 MT c2 MT

Finished writing norms

Attaching package: 'BSgenome.Hsapiens.UCSC.hg38'

The following object is masked from 'package:BSgenome.Hsapiens.UCSC.hg19':

    Hsapiens

Using chr22and cut patterns GATC
Joining, by = "bins"
Joining, by = "bins"
Joining, by = "bins"
WARN [2022-04-12T11:21:56,207]  [Globals.java:138] [main]  Development mode is enabled
Warning in add_2D_features(gi_list[[chrom]], count_matrix) :
  Bins and counts mismatch. This will slow down the
            performance of counts integration.Check if genome and/or bin size of
            counts data is aligned with the GenomicInteractions object.
Chromosome chr22 intrachromosomal counts processed.
Chromosome chr22 complete.
WARN [2022-04-12T11:22:04,355]  [Globals.java:138] [main]  Development mode is enabled
Chromosome chr22 intrachromosomal counts processed.
Chromosome chr22 complete.
WARN [2022-04-12T11:22:10,552]  [Globals.java:138] [main]  Development mode is enabled
Chromosome chr22 intrachromosomal counts processed.
Chromosome chr22 complete.
WARN [2022-04-12T11:22:17,121]  [Globals.java:138] [main]  Development mode is enabled
Chromosome chr22 intrachromosomal counts processed.
Chromosome chr22 complete.
Joining, by = c("Dband", "chr", "startI", "startJ")
Joining, by = c("Dband", "chr", "startI", "startJ")
Joining, by = c("Dband", "chr", "startI", "startJ")
Joining, by = "Dband"
converting counts to integer mode
WARN [2022-04-12T11:22:39,183]  [Globals.java:138] [main]  Development mode is enabled
Start filtering  ...2022-04-12 11:22:46
Filter out 342 rows and columns ...
Start Iterative Correction ...
it=1 2022-04-12 11:22:47
it=2 2022-04-12 11:22:47
it=3 2022-04-12 11:22:48
it=4 2022-04-12 11:22:48
it=5 2022-04-12 11:22:48
it=6 2022-04-12 11:22:48
it=7 2022-04-12 11:22:48
it=8 2022-04-12 11:22:48
it=9 2022-04-12 11:22:49
it=10 2022-04-12 11:22:49
Did not converged. Stop at iteration 10